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Archer, the son of famed warp engineer Henry Archer and his wife Sally, was born in 2112 in Upstate New York, where he spent most of his formative years; he later claimed to have spent the majority of his life in San Francisco. The second season episode "First Flight" depicted in flashback that he spent many years as a test pilot in the nascent Starfleet's NX program, based in San Francisco. His dreams of exploring started as a boy. As a youth, Archer earned the Eagle Scout Award, along with 26 Merit Badges, from the Boy Scouts of America he is an avid Water polo fan often relaxing by watching water polo games.

Archer grew up with a distrust of Vulcans, perceiving them as having held back Humanity's progress, particularly with regard to his father's warp five engine.

As a commander in Starfleet, Archer served as a pilot in the NX warp trials with A.G. Robinson, Duvall and Gardner (all mentioned in the episode "First Flight"; it is assumed it is this Gardner who becomes Admiral when Maxwell Forrest dies in "The Forge"). Robinson pushed the limits of a test ship, the NX-Alpha, resulting in its destruction. The Vulcans recommended that the warp trials end, which Starfleet agreed to until Charles Tucker III (who would later serve as chief engineer under Archer) fixed the intermix ratios, and Archer and Robinson stole the NX-Beta, the second test ship, to prove its readiness. Although Archer was suspended for the act, it is believed his risk (and the fact that it paid off) eventually secured his role as Captain of Enterprise, Earth's first warp five starship.

As a man who loves to travel amongst the stars, Archer realizes being captain is a larger duty than manager and astronomer. He runs into species from all over the quadrant trying to kill him and his crew. Encounters with the Mazarites, Tholians, Suliban and Klingons cause Archer to become more of a military commander.

In addition, Archer learns that the duties of captain include being a diplomat. During Seasons 1 and 2, he is somewhat uncomfortable with this role, especially in the episode "A Night In Sickbay" when Porthos contracts a deadly illness on an alien world.

While exploring, Archer becomes an enemy of the Klingons. In a dispute with the Klingon Empire in 2152, he is convicted and sentenced to exile on Rura Penthe, even though he is innocent of the charges and despite the Klingons having acknowledged his previous service to the Empire. With his escape, a bounty is put on Archer's head and tensions with the Klingon Empire increase.

Although initially optimistic, Archer becomes involved in his first mission as captain of Enterprise in the middle of the Temporal Cold War. The Temporal Cold War begins at the beginning of the pilot episode, "Broken Bow". In that episode, the audience is introduced to the Suliban and a mysterious being from the future (informally referred to as "Future Guy") who is guiding them.

As the Temporal Cold War continues, Archer also meets Daniels, whose purpose seemingly is to safeguard Archer in particular and Enterprise in general. Daniels' comments are that Archer will be the man who helps to form the United Federation of Planets, and it becomes apparent by the third season that Daniels is representing the Federation throughout the Temporal Cold War.

In Season 3, he was the Military commander in the Expanse. Following the Xindi attack on Earth in 2153, Archer becomes a changed man. No longer a congenial captain, he is now driven and determined to seek out and confront the perpetrators. Archer commits desperate, controversial acts of questionable morality to ensure a future for Earth, including torturing a prisoner, cloning Tucker to harvest body parts in order to save the chief engineer and thus killing the clone, and stealing a vital warp coil and leaving a ship of aliens stranded in space.

After returning home in 2154, Archer helps a faction of Vulcans fight an oppressive government on their planet. During this incident, he is the recipient of the katra, or living spirit, of the great Vulcan philosopher Surak. The katra is later transferred to a Vulcan priest, and Archer is left unharmed. This leads to the reformation of Vulcan society, and explains why the Vulcans of Archer's time were so different from the Vulcans of Kirk's time. In the process, Archer becomes the first known Human participant in a Vulcan mind meld. Since that experience, he has used that knowledge at least once: To assist T'Pol with conducting her first mind meld in order to gain information about who kidnapped Dr. Phlox (as seen in the episode "Affliction").

Archer is also involved in one of the first, and possibly most significant, treaties yet, being asked to escort Gral, the Tellarite ambassador, to the Tellarite-Andorian negotiations. En route, he and his crew run into the Andorian Shran, a long-time friend/enemy/ally. During Shran's stay, Romulans attack and cause the fragile alliance to crash to a halt. In the mix-up, a Tellarite kills Shran's lover Talas, and Shran avenges her death by demanding the Tellarite who killed her to fight to the death. In an attempt to protect the fragile peace treaty, Archer takes the challenge instead and Shran is incapacitated (but not seriously hurt). The alliance remains intact, and soon evolves into the United Federation of Planets. ("Babel One", "United", "The Aenar", "Demons", "Terra Prime", "These Are the Voyages...")

The time traveler Daniels revealed that Archer would eventually have a major role in the founding of the United Federation of Planets in 2161. He briefly took Archer ahead in time to the point where Archer is about to sign the Federation accords on Earth.

Archer's fate is revealed in the episode "In a Mirror, Darkly Part II" when a computer information screen aboard the 23rd century Starfleet vessel USS Defiant is briefly visible. According to the computer profile, Archer was an Admiral and Chief of Staff at Starfleet Command at the time of his retirement. He later went on to serve as ambassador to Andoria from 2165 to 2175. From 2175 to 2183, Archer served as a member of the Federation Council, followed by eight years as Federation President (2184–2192). He was also an honorary member of the Andorian Imperial Guard.

Unused artwork shows that Archer dies peacefully in his sleep at his home in Upstate New York in 2245, exactly one day after he attends the commissioning ceremony of the USS Enterprise (NCC-1701). However, this computer display gives 2160 as the year Archer's captaincy of Enterprise came to an end, which is contradicted by the 2161 date given in "These Are the Voyages...".

The 2009 Star Trek film briefly references Archer, as Montgomery Scott receives punishment stemming from an incident involving a transporter and "Admiral Archer's prized Beagle." There was some confusion as to if this actually referred to Jonathan Archer himself as this would make him 141 years old. Star Trek writer Bob Orci went on record to clear up the issue, "...Admiral Archer is a reference to the Archer we all know and love, and yes he would be over 100, which is a likely life expectancy in a futuristic space faring race of humans (as depicted by McCoy’s (DeForest Kelley) in The Next Generation.)" [1]

Porthos is Archer's pet dog. One of four males born in a litter of EnglishBeagles, Porthos and his brothers, Athos, Aramis and d'Artagnan, were named after characters from The Three Musketeers by Alexandre Dumas, père. He has been Archer's faithful companion since the age of six weeks, and has remained so for the duration of Archer's 10-year assignment as captain of Enterprise.

Porthos was portrayed by a male beagle named Prada in Season 1. Afterwards, he was played by a further two female beagles, Breezy and Windy, although the character of Porthos remained male. Prada also portrayed the character Lou in the film Cats & Dogs.

Archer would occasionally leave Porthos in the care of Dr. Phlox when he was away or otherwise unavailable.

In Season 3 Episode 10 Archer explains in answer to the question "Can he do any tricks?" that "I haven’t taught him any, mostly what he does is eat, sleep and not fetch." He also commented “there’s nothing Porthos likes more than dinner time".

Although Porthos isn't the first domesticated pet to be featured in a Star Trek series (Data owned a cat, Spot, in Star Trek: The Next Generation and Captain Jean-Luc Picard owned a lionfish named Livingston), Porthos has the distinction of being the first pet to maintain an ongoing presence in the series, and even – as illustrated above – become the focus of an episode.

In the episode "Acquisition", Porthos was interrogated by a group of Ferengi pirates while the rest of the crew were incapacitated, but the aliens' universal translator could not decipher his barking. The pirates didn't know what to make of the dog, even speculating that he was perhaps food. They then decided they could sell him to a zoo.

In the 2009 Star Trek film, it is implied that "Admiral Archer's" prized Beagle was involved in a freak accident when Montgomery Scott used him as a test subject for a transporter experiment. However, Porthos would have been over 70 years old when Scott was born, therefore it is not at all certain whether or not the beagle in question was Porthos, although it is possible that it has been made possible for dogs to live longer by that time; it's also possible that Archer only kept beagles for pets. The novelization of the film has the beagle transported onto the Enterprise.

Like most characters in the Terran Empire, the mirror Archer was treacherous, cunning and scheming. He led a mutiny against Forrest and took over Enterprise. However, with the help of T'Pol and other Vulcans, Forrest was freed and retook the ship. Archer surrendered, but had locked the ship's navigation controls so its heading could not be altered. His reason for the mutiny was brought to light as he had been informed about a ship that seemed to be from another dimension. With the ship's course unable to be changed and Starfleet now intrigued by what Archer had become aware of, Forrest was ordered to investigate, he also had Archer punished in the Agony Booth for a then record of ten hours, giving the Commander only one hour to clean up and get ready for a staff meeting after his release. On arrival, they discovered the USS Defiant, a Starfleet ship from 100 years into the future of the "normal" universe.

Archer led an away team to take control of the Defiant while the Enterprise was destroyed by the Tholians. He and his team, plus survivors from the Enterprise, discovered the Defiant was not only from another dimension, but the future and that the alternate dimension never had a Terran Empire. After successfully crushing a rebellion against the Empire, Archer attempted to take the futuristic vessel to Earth where he would proclaim himself Emperor. However, before he could do so, he was killed by his universe's Hoshi Sato, who poisoned him, took the ship and (we are led to believe) the Terran throne as well for herself.